On Aug 29, 2012, at 12:41 PM, Douglas W Cloud wrote:
Hello all, I am trying to get a Galaxy server configured to submit jobs to an LSF cluster running version 7 update 2, generally CentOS/Redhat 5 systems. I have the Galaxy host as a client in LSF, but when I tried to configure/make/install the FedStage drmaa code, it errors out in the make stage (see stdout below). Don't know what to fix, if it's possible.
If anyone has experience configuring/troubleshooting this code to get Galaxy conversant with LSF, I'd appreciate any feedback. Thanks!
Regards, Doug _________
util.c: In function 'lsfdrmaa_map_lsberrno': util.c:730: error: 'LSBE_ADRSV_ID_UNIQUE' undeclared (first use in this function) util.c:730: error: (Each undeclared identifier is reported only once util.c:730: error: for each function it appears in.) util.c:731: error: 'LSBE_BAD_RSVNAME' undeclared (first use in this function) util.c:732: error: 'LSBE_BAD_CHKPNTDIR' undeclared (first use in this function) util.c:734: error: 'LSBE_JOB_REQUEUE_BADEXCLUDE' undeclared (first use in this function) util.c:737: error: 'LSBE_ADVRSV_ACTIVESTART' undeclared (first use in this function) util.c:739: error: 'LSBE_ADRSV_ID_USED' undeclared (first use in this function) util.c:740: error: 'LSBE_ADRSV_PREVDISABLED' undeclared (first use in this function) util.c:742: error: 'LSBE_ADRSV_DISABLECURR' undeclared (first use in this function) util.c:744: error: 'LSBE_ADRSV_NOT_RSV_HOST' undeclared (first use in this function) util.c:749: error: 'LSBE_ADRSV_MOD_REMOTE' undeclared (first use in this function) util.c:751: error: 'LSBE_JOB_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:752: error: 'LSBE_APP_RUSAGE_EXCEED_LIMIT' undeclared (first use in this function) util.c:755: error: 'LSBE_ADRSV_DISABLE_DATE' undeclared (first use in this function) util.c:759: error: 'LSBE_ADRSV_DETACH_MIX' undeclared (first use in this function) util.c:761: error: 'LSBE_ADRSV_DETACH_ACTIVE' undeclared (first use in this function) util.c:765: error: 'LSBE_MISSING_START_END_TIME' undeclared (first use in this function) make[3]: *** [libdrmaa_la-util.lo] Error 1 make[3]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[2]: *** [all] Error 2 make[2]: Leaving directory `/root/installers/lsf_drmaa-1.0.4/lsf_drmaa' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/root/installers/lsf_drmaa-1.0.4'
Hi Doug,
It looks like you probably need to include whatever header file from LSF contains these declarations. I don't have an LSF installation so I don't know what file that is, but it would presumably be with the other LSF includes.
You may also want to contact the lsf-drmaa developers or Platform for more specific support.
--nate
(Same output with version 1.0.3.)
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